graph TD
  subgraph Input data
    A[Extant genomes]
    B[Species tree]
    C[Gene phylogenies]
    D[Extant gene orders]
  end
  subgraph AGORA
    E[Ancestral gene lists]
    F{{Pairwise comparisons}}
    G[Ancestral adjacency graph]
    H{{Graph linearisation}}
    J{{Block assembly}}
  end
  subgraph Output
    K[Ancestral Genomes]
  end
  A -.- B & C & D
  C --> E
  B --> J & F
  D --> F & J
  E --> F --> G --> H --> J --> K
